mirror of
https://github.com/samply/bridgehead.git
synced 2025-11-04 06:00:18 +01:00
457 lines
16 KiB
Bash
457 lines
16 KiB
Bash
#!/bin/bash -e
|
|
|
|
detectCompose() {
|
|
if [[ "$(docker compose version 2>/dev/null)" == *"Docker Compose version"* ]]; then
|
|
COMPOSE="docker compose"
|
|
else
|
|
COMPOSE="docker-compose"
|
|
# This is intended to fail on startup in the next prereq check.
|
|
fi
|
|
}
|
|
|
|
setupProxy() {
|
|
### Note: As the current data protection concepts do not allow communication via HTTP,
|
|
### we are not setting a proxy for HTTP requests.
|
|
|
|
local http="no"
|
|
local https="no"
|
|
if [ $HTTPS_PROXY_URL ]; then
|
|
local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
|
|
local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
|
|
local hostport=$(echo $HTTPS_PROXY_URL | sed -e "s,$proto,,g" | cut -d/ -f1)
|
|
HTTPS_PROXY_HOST="$(echo $hostport | sed -e 's,:.*,,g')"
|
|
HTTPS_PROXY_PORT="$(echo $hostport | sed -e 's,^.*:,:,g' -e 's,.*:\([0-9]*\).*,\1,g' -e 's,[^0-9],,g')"
|
|
if [[ ! -z "$HTTPS_PROXY_USERNAME" && ! -z "$HTTPS_PROXY_PASSWORD" ]]; then
|
|
local proto="$(echo $HTTPS_PROXY_URL | grep :// | sed -e 's,^\(.*://\).*,\1,g')"
|
|
local fqdn="$(echo ${HTTPS_PROXY_URL/$proto/})"
|
|
HTTPS_PROXY_FULL_URL="$(echo $proto$HTTPS_PROXY_USERNAME:$HTTPS_PROXY_PASSWORD@$fqdn)"
|
|
https="authenticated"
|
|
else
|
|
HTTPS_PROXY_FULL_URL=$HTTPS_PROXY_URL
|
|
https="unauthenticated"
|
|
fi
|
|
fi
|
|
|
|
log INFO "Configuring proxy servers: $http http proxy (we're not supporting unencrypted comms), $https https proxy"
|
|
export HTTPS_PROXY_HOST HTTPS_PROXY_PORT HTTPS_PROXY_FULL_URL
|
|
}
|
|
|
|
exitIfNotRoot() {
|
|
if [ "$EUID" -ne 0 ]; then
|
|
log "ERROR" "Please run as root"
|
|
fail_and_report 1 "Please run as root"
|
|
fi
|
|
}
|
|
|
|
checkOwner(){
|
|
COUNT=$(find $1 ! -user $2 |wc -l)
|
|
if [ $COUNT -gt 0 ]; then
|
|
log ERROR "$COUNT files in $1 are not owned by user $2. Run find $1 ! -user $2 to see them, chown -R $2 $1 to correct this issue."
|
|
return 1
|
|
fi
|
|
return 0
|
|
}
|
|
|
|
printUsage() {
|
|
echo "Usage: bridgehead start|stop|logs|docker-logs|is-running|update|check|install|uninstall|adduser|enroll PROJECTNAME"
|
|
echo "PROJECTNAME should be one of ccp|bbmri|cce|itcc|kr|dhki|nngm"
|
|
}
|
|
|
|
checkRequirements() {
|
|
if ! lib/prerequisites.sh $@; then
|
|
log "ERROR" "Validating Prerequisites failed, please fix the error(s) above this line."
|
|
fail_and_report 1 "Validating prerequisites failed."
|
|
else
|
|
return 0
|
|
fi
|
|
}
|
|
|
|
fetchVarsFromVault() {
|
|
[ -e /etc/bridgehead/vault.conf ] && source /etc/bridgehead/vault.conf
|
|
|
|
if [ -z "$BW_MASTERPASS" ] || [ -z "$BW_CLIENTID" ] || [ -z "$BW_CLIENTSECRET" ]; then
|
|
log "ERROR" "Please supply correct credentials in /etc/bridgehead/vault.conf."
|
|
return 1
|
|
fi
|
|
|
|
set +e
|
|
|
|
PASS=$(BW_MASTERPASS="$BW_MASTERPASS" BW_CLIENTID="$BW_CLIENTID" BW_CLIENTSECRET="$BW_CLIENTSECRET" docker run --rm -e BW_MASTERPASS -e BW_CLIENTID -e BW_CLIENTSECRET -e http_proxy docker.verbis.dkfz.de/cache/samply/bridgehead-vaultfetcher:latest $@)
|
|
RET=$?
|
|
|
|
if [ $RET -ne 0 ]; then
|
|
echo "Code: $RET"
|
|
echo $PASS
|
|
return $RET
|
|
fi
|
|
|
|
eval $(echo -e "$PASS" | sed 's/\r//g')
|
|
|
|
set -e
|
|
|
|
return 0
|
|
}
|
|
|
|
fetchVarsFromVaultByFile() {
|
|
VARS_TO_FETCH=""
|
|
|
|
for line in $(cat $@); do
|
|
if [[ $line =~ .*=[\"]*\<VAULT\>[\"]*.* ]]; then
|
|
VARS_TO_FETCH+="$(echo -n $line | sed 's/=.*//') "
|
|
fi
|
|
done
|
|
|
|
if [ -z "$VARS_TO_FETCH" ]; then
|
|
return 0
|
|
fi
|
|
|
|
log INFO "Fetching $(echo $VARS_TO_FETCH | wc -w) secrets from Vault ..."
|
|
|
|
fetchVarsFromVault $VARS_TO_FETCH
|
|
|
|
return 0
|
|
}
|
|
|
|
assertVarsNotEmpty() {
|
|
MISSING_VARS=""
|
|
|
|
for VAR in $@; do
|
|
if [ -z "${!VAR}" ]; then
|
|
MISSING_VARS+="$VAR "
|
|
fi
|
|
done
|
|
|
|
if [ -n "$MISSING_VARS" ]; then
|
|
log "ERROR" "Mandatory variables not defined: $MISSING_VARS"
|
|
return 1
|
|
fi
|
|
|
|
return 0
|
|
}
|
|
|
|
fixPermissions() {
|
|
CHOWN=$(which chown)
|
|
sudo $CHOWN -R bridgehead /etc/bridgehead /srv/docker/bridgehead
|
|
}
|
|
|
|
source lib/monitoring.sh
|
|
|
|
report_error() {
|
|
CODE=$1
|
|
shift
|
|
log ERROR "$@"
|
|
hc_send $CODE "$@"
|
|
}
|
|
|
|
fail_and_report() {
|
|
report_error $@
|
|
exit $1
|
|
}
|
|
|
|
setHostname() {
|
|
if [ -z "$HOST" ]; then
|
|
export HOST=$(hostname -f | tr "[:upper:]" "[:lower:]")
|
|
log DEBUG "Using auto-detected hostname $HOST."
|
|
fi
|
|
}
|
|
|
|
# This function optimizes the usage of memory through blaze, according to the official performance tuning guide:
|
|
# https://github.com/samply/blaze/blob/master/docs/tuning-guide.md
|
|
# Short summary of the adjustments made:
|
|
# - set blaze memory cap to a quarter of the system memory
|
|
# - set db block cache size to a quarter of the system memory
|
|
# - limit resource count allowed in blaze to 1,25M per 4GB available system memory
|
|
optimizeBlazeMemoryUsage() {
|
|
if [ -z "$BLAZE_MEMORY_CAP" ]; then
|
|
system_memory_in_mb=$(LC_ALL=C free -m | grep 'Mem:' | awk '{print $2}');
|
|
export BLAZE_MEMORY_CAP=$(($system_memory_in_mb/4));
|
|
fi
|
|
if [ -z "$BLAZE_RESOURCE_CACHE_CAP" ]; then
|
|
available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
|
|
if [ $available_system_memory_chunks -eq 0 ]; then
|
|
log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
|
|
export BLAZE_RESOURCE_CACHE_CAP=128000;
|
|
export BLAZE_CQL_CACHE_CAP=32;
|
|
else
|
|
export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
|
|
export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
|
|
fi
|
|
fi
|
|
}
|
|
|
|
# Takes 1) The Backup Directory Path 2) The name of the Service to be backuped
|
|
# Creates 3 Backups: 1) For the past seven days 2) For the current month and 3) for each calendar week
|
|
createEncryptedPostgresBackup(){
|
|
docker exec "$2" bash -c 'pg_dump -U $POSTGRES_USER $POSTGRES_DB --format=p --no-owner --no-privileges' | \
|
|
# TODO: Encrypt using /etc/bridgehead/pki/${SITE_ID}.priv.pem | \
|
|
tee "$1/$2/$(date +Last-%A).sql" | \
|
|
tee "$1/$2/$(date +%Y-%m).sql" > \
|
|
"$1/$2/$(date +%Y-KW%V).sql"
|
|
}
|
|
|
|
|
|
# from: https://gist.github.com/sj26/88e1c6584397bb7c13bd11108a579746
|
|
# ex. use: retry 5 /bin/false
|
|
function retry {
|
|
local retries=$1
|
|
shift
|
|
|
|
local count=0
|
|
until "$@"; do
|
|
exit=$?
|
|
wait=$((2 ** $count))
|
|
count=$(($count + 1))
|
|
if [ $count -lt $retries ]; then
|
|
echo "Retry $count/$retries exited with code $exit, retrying in $wait seconds..."
|
|
sleep $wait
|
|
else
|
|
echo "Retry $count/$retries exited with code $exit, giving up."
|
|
return $exit
|
|
fi
|
|
done
|
|
return 0
|
|
}
|
|
|
|
function bk_is_running {
|
|
detectCompose
|
|
RUNNING="$($COMPOSE -p $PROJECT -f minimal/docker-compose.yml -f ./$PROJECT/docker-compose.yml $OVERRIDE ps -q)"
|
|
NUMBEROFRUNNING=$(echo "$RUNNING" | wc -l)
|
|
if [ $NUMBEROFRUNNING -ge 2 ]; then
|
|
return 0
|
|
else
|
|
return 1
|
|
fi
|
|
}
|
|
|
|
function do_enroll_inner {
|
|
PARAMS=""
|
|
|
|
MANUAL_PROXY_ID="${1:-$PROXY_ID}"
|
|
if [ -z "$MANUAL_PROXY_ID" ]; then
|
|
log ERROR "No Proxy ID set"
|
|
exit 1
|
|
else
|
|
log INFO "Enrolling Beam Proxy Id $MANUAL_PROXY_ID"
|
|
fi
|
|
|
|
SUPPORT_EMAIL="${2:-$SUPPORT_EMAIL}"
|
|
if [ -n "$SUPPORT_EMAIL" ]; then
|
|
PARAMS+="--admin-email $SUPPORT_EMAIL"
|
|
fi
|
|
|
|
docker run --rm -v /etc/bridgehead/pki:/etc/bridgehead/pki docker.verbis.dkfz.de/cache/samply/beam-enroll:latest --output-file $PRIVATEKEYFILENAME --proxy-id $MANUAL_PROXY_ID $PARAMS
|
|
chmod 600 $PRIVATEKEYFILENAME
|
|
}
|
|
|
|
function do_enroll {
|
|
do_enroll_inner $@
|
|
}
|
|
|
|
add_basic_auth_user() {
|
|
USER="${1}"
|
|
PASSWORD="${2}"
|
|
NAME="${3}"
|
|
PROJECT="${4}"
|
|
FILE="/etc/bridgehead/${PROJECT}.local.conf"
|
|
ENCRY_CREDENTIALS="$(docker run --rm docker.verbis.dkfz.de/cache/httpd:alpine htpasswd -nb $USER $PASSWORD | tr -d '\n' | tr -d '\r')"
|
|
if [ -f $FILE ] && grep -R -q "$NAME=" $FILE # if a specific basic auth user already exists:
|
|
then
|
|
sed -i "/$NAME/ s|='|='$ENCRY_CREDENTIALS,|" $FILE
|
|
else
|
|
echo -e "\n## Basic Authentication Credentials for:\n$NAME='$ENCRY_CREDENTIALS'" >> $FILE;
|
|
fi
|
|
log DEBUG "Saving clear text credentials in $FILE. If wanted, delete them manually."
|
|
sed -i "/^$NAME/ s|$|\n# User: $USER\n# Password: $PASSWORD|" $FILE
|
|
}
|
|
|
|
OIDC_PUBLIC_REDIRECT_URLS=${OIDC_PUBLIC_REDIRECT_URLS:-""}
|
|
OIDC_PRIVATE_REDIRECT_URLS=${OIDC_PRIVATE_REDIRECT_URLS:-""}
|
|
|
|
# Add a redirect url to the public oidc client of the bridgehead
|
|
function add_public_oidc_redirect_url() {
|
|
if [[ $OIDC_PUBLIC_REDIRECT_URLS == "" ]]; then
|
|
OIDC_PUBLIC_REDIRECT_URLS+="$(generate_redirect_urls $1)"
|
|
else
|
|
OIDC_PUBLIC_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
|
|
fi
|
|
}
|
|
|
|
# Add a redirect url to the private oidc client of the bridgehead
|
|
function add_private_oidc_redirect_url() {
|
|
if [[ $OIDC_PRIVATE_REDIRECT_URLS == "" ]]; then
|
|
OIDC_PRIVATE_REDIRECT_URLS+="$(generate_redirect_urls $1)"
|
|
else
|
|
OIDC_PRIVATE_REDIRECT_URLS+=",$(generate_redirect_urls $1)"
|
|
fi
|
|
}
|
|
|
|
function sync_secrets() {
|
|
local delimiter=$'\x1E'
|
|
local secret_sync_args=""
|
|
if [[ $OIDC_PRIVATE_REDIRECT_URLS != "" ]]; then
|
|
secret_sync_args="OIDC:OIDC_CLIENT_SECRET:private;$OIDC_PRIVATE_REDIRECT_URLS"
|
|
fi
|
|
if [[ $OIDC_PUBLIC_REDIRECT_URLS != "" ]]; then
|
|
if [[ $secret_sync_args == "" ]]; then
|
|
secret_sync_args="OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
|
|
else
|
|
secret_sync_args+="${delimiter}OIDC:OIDC_PUBLIC:public;$OIDC_PUBLIC_REDIRECT_URLS"
|
|
fi
|
|
fi
|
|
if [[ $secret_sync_args == "" ]]; then
|
|
return
|
|
fi
|
|
|
|
if [ "$PROJECT" == "bbmri" ]; then
|
|
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
|
|
proxy_id=$ERIC_PROXY_ID
|
|
broker_url=$ERIC_BROKER_URL
|
|
broker_id=$ERIC_BROKER_ID
|
|
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
|
|
else
|
|
proxy_id=$PROXY_ID
|
|
broker_url=$BROKER_URL
|
|
broker_id=$BROKER_ID
|
|
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
|
|
fi
|
|
|
|
mkdir -p /var/cache/bridgehead/secrets/ || fail_and_report 1 "Failed to create '/var/cache/bridgehead/secrets/'. Please run sudo './bridgehead install $PROJECT' again."
|
|
touch /var/cache/bridgehead/secrets/oidc
|
|
docker run --rm \
|
|
-v /var/cache/bridgehead/secrets/oidc:/usr/local/cache \
|
|
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
|
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
|
|
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
|
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
|
-e NO_PROXY=localhost,127.0.0.1 \
|
|
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
|
-e PROXY_ID=$proxy_id \
|
|
-e BROKER_URL=$broker_url \
|
|
-e OIDC_PROVIDER=secret-sync-central.test-secret-sync.$broker_id \
|
|
-e SECRET_DEFINITIONS=$secret_sync_args \
|
|
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
|
|
|
set -a # Export variables as environment variables
|
|
source /var/cache/bridgehead/secrets/oidc
|
|
set +a # Export variables in the regular way
|
|
}
|
|
|
|
function secret_sync_gitlab_token() {
|
|
if [ "$PROJECT" == "minimal" ]; then
|
|
log "INFO" "Not running Secret Sync for project minimal"
|
|
return
|
|
fi
|
|
# Map the origin of the git repository /etc/bridgehead to the prefix recognized by Secret Sync
|
|
local gitlab
|
|
case "$(git -C /etc/bridgehead remote get-url origin)" in
|
|
*git.verbis.dkfz.de*) gitlab=verbis;;
|
|
*gitlab.bbmri-eric.eu*) gitlab=bbmri;;
|
|
*)
|
|
log "WARN" "Not running Secret Sync because the git repository /etc/bridgehead has unknown origin"
|
|
return
|
|
;;
|
|
esac
|
|
|
|
if [ "$PROJECT" == "bbmri" ]; then
|
|
# If the project is BBMRI, use the BBMRI-ERIC broker and not the GBN broker
|
|
proxy_id=$ERIC_PROXY_ID
|
|
broker_url=$ERIC_BROKER_URL
|
|
broker_id=$ERIC_BROKER_ID
|
|
root_crt_file="/srv/docker/bridgehead/bbmri/modules/${ERIC_ROOT_CERT}.root.crt.pem"
|
|
else
|
|
proxy_id=$PROXY_ID
|
|
broker_url=$BROKER_URL
|
|
broker_id=$BROKER_ID
|
|
root_crt_file="/srv/docker/bridgehead/$PROJECT/root.crt.pem"
|
|
fi
|
|
|
|
# Create a temporary directory for Secret Sync that is valid per boot
|
|
secret_sync_tempdir="/tmp/bridgehead/secret-sync.boot-$(cat /proc/sys/kernel/random/boot_id)"
|
|
mkdir -p $secret_sync_tempdir
|
|
|
|
# Use Secret Sync to validate the GitLab token in $secret_sync_tempdir/cache.
|
|
# If it is missing or expired, Secret Sync will create a new token and write it to the file.
|
|
# The git credential helper reads the token from the file during git pull.
|
|
log "INFO" "Running Secret Sync for the GitLab token (gitlab=$gitlab)"
|
|
docker pull docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest # make sure we have the latest image
|
|
docker run --rm \
|
|
-v $PRIVATEKEYFILENAME:/run/secrets/privkey.pem:ro \
|
|
-v $root_crt_file:/run/secrets/root.crt.pem:ro \
|
|
-v /etc/bridgehead/trusted-ca-certs:/conf/trusted-ca-certs:ro \
|
|
-v $secret_sync_tempdir:/secret-sync/ \
|
|
-e CACHE_PATH=/secret-sync/gitlab-token \
|
|
-e TLS_CA_CERTIFICATES_DIR=/conf/trusted-ca-certs \
|
|
-e NO_PROXY=localhost,127.0.0.1 \
|
|
-e ALL_PROXY=$HTTPS_PROXY_FULL_URL \
|
|
-e PROXY_ID=$proxy_id \
|
|
-e BROKER_URL=$broker_url \
|
|
-e GITLAB_PROJECT_ACCESS_TOKEN_PROVIDER=secret-sync-central.central-secret-sync.$broker_id \
|
|
-e SECRET_DEFINITIONS=GitLabProjectAccessToken:BRIDGEHEAD_CONFIG_REPO_TOKEN:$gitlab \
|
|
docker.verbis.dkfz.de/cache/samply/secret-sync-local:latest
|
|
if [ $? -eq 0 ]; then
|
|
log "INFO" "Secret Sync was successful"
|
|
# In the past we used to hardcode tokens into the repository URL. We have to remove those now for the git credential helper to become effective.
|
|
CLEAN_REPO="$(git -C /etc/bridgehead remote get-url origin | sed -E 's|https://[^@]+@|https://|')"
|
|
git -C /etc/bridgehead remote set-url origin "$CLEAN_REPO"
|
|
# Set the git credential helper
|
|
git -C /etc/bridgehead config credential.helper /srv/docker/bridgehead/lib/gitlab-token-helper.sh
|
|
else
|
|
log "WARN" "Secret Sync failed"
|
|
# Remove the git credential helper
|
|
git -C /etc/bridgehead config --unset credential.helper
|
|
fi
|
|
|
|
# In the past the git credential helper was also set for /srv/docker/bridgehead but never used.
|
|
# Let's remove it to avoid confusion. This line can be removed at some point the future when we
|
|
# believe that it was removed on all/most production servers.
|
|
git -C /srv/docker/bridgehead config --unset credential.helper
|
|
}
|
|
|
|
capitalize_first_letter() {
|
|
input="$1"
|
|
capitalized="$(tr '[:lower:]' '[:upper:]' <<< ${input:0:1})${input:1}"
|
|
echo "$capitalized"
|
|
}
|
|
|
|
# Generate a string of ',' separated string of redirect urls relative to $HOST.
|
|
# $1 will be appended to the url
|
|
# If the host looks like dev-jan.inet.dkfz-heidelberg.de it will generate urls with dev-jan and the original $HOST as url Authorities
|
|
function generate_redirect_urls(){
|
|
local redirect_urls="https://${HOST}$1"
|
|
local host_without_proxy="$(echo "$HOST" | cut -d '.' -f1)"
|
|
# Only append second url if its different and the host is not an ip address
|
|
if [[ "$HOST" != "$host_without_proxy" && ! "$HOST" =~ ^[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
|
|
redirect_urls+=",https://$host_without_proxy$1"
|
|
fi
|
|
echo "$redirect_urls"
|
|
}
|
|
|
|
# This password contains at least one special char, a random number and a random upper and lower case letter
|
|
generate_password(){
|
|
local seed_text="$1"
|
|
local seed_num=$(awk 'BEGIN{FS=""} NR==1{print $10}' /etc/bridgehead/pki/${SITE_ID}.priv.pem | od -An -tuC)
|
|
local nums="1234567890"
|
|
local n=$(echo "$seed_num" | awk '{print $1 % 10}')
|
|
local random_digit=${nums:$n:1}
|
|
local n=$(echo "$seed_num" | awk '{print $1 % 26}')
|
|
local upper="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
|
|
local lower="abcdefghijklmnopqrstuvwxyz"
|
|
local random_upper=${upper:$n:1}
|
|
local random_lower=${lower:$n:1}
|
|
local n=$(echo "$seed_num" | awk '{print $1 % 8}')
|
|
local special='@#$%^&+='
|
|
local random_special=${special:$n:1}
|
|
|
|
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
|
|
local main_password=$(echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/\//A/g')
|
|
|
|
echo "${main_password}${random_digit}${random_upper}${random_lower}${random_special}"
|
|
}
|
|
|
|
# This password only contains alphanumeric characters
|
|
generate_simple_password(){
|
|
local seed_text="$1"
|
|
local combined_text="This is a salt string to generate one consistent password for ${seed_text}. It is not required to be secret."
|
|
echo "${combined_text}" | sha1sum | openssl pkeyutl -sign -inkey "/etc/bridgehead/pki/${SITE_ID}.priv.pem" 2> /dev/null | base64 | head -c 26 | sed 's/[+\/]/A/g'
|
|
}
|